Polygenic Score (PGS) ID: PGS001341

Predicted Trait
Reported Trait Asthma
Mapped Trait(s) asthma (MONDO_0004979)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC382
Released in PGS Catalog: Oct. 21, 2021
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name GBE_HC382
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 6,430
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
269,704 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
—
[
  • 36,294 cases
  • , 233,410 controls
]
 European UKB — — — white British ancestry —

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM) 		PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM009191 PSS004466|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Asthma — AUROC: 0.61763 [0.59798, 0.63728] R²: 0.03727
Incremental AUROC (full-covars): 0.0081
PGS R2 (no covariates): 0.00847
PGS AUROC (no covariates): 0.55669 [0.53574, 0.57763]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009192 PSS004467|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Asthma — AUROC: 0.57795 [0.53557, 0.62032] R²: 0.02196
Incremental AUROC (full-covars): -0.01536
PGS R2 (no covariates): 0.00014
PGS AUROC (no covariates): 0.51559 [0.47138, 0.55979]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009193 PSS004468|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Asthma — AUROC: 0.63649 [0.62628, 0.6467] R²: 0.04868
Incremental AUROC (full-covars): 0.06379
PGS R2 (no covariates): 0.0373
PGS AUROC (no covariates): 0.6175 [0.60705, 0.62795]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009194 PSS004469|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Asthma — AUROC: 0.60865 [0.59116, 0.62614] R²: 0.03337
Incremental AUROC (full-covars): 0.03258
PGS R2 (no covariates): 0.01973
PGS AUROC (no covariates): 0.58188 [0.5641, 0.59966]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009195 PSS004470|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Asthma — AUROC: 0.62569 [0.61945, 0.63192] R²: 0.04404
Incremental AUROC (full-covars): 0.07406
PGS R2 (no covariates): 0.03731
PGS AUROC (no covariates): 0.61664 [0.61037, 0.62291]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

Evaluated Samples

PGS Sample Set ID
(PSS) 		Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS004466 — —
[
  • 871 cases
  • , 5,626 controls
]
 — African unspecified — UKB —
PSS004467 — —
[
  • 166 cases
  • , 1,538 controls
]
 — East Asian — UKB —
PSS004468 — —
[
  • 3,243 cases
  • , 21,662 controls
]
 — European non-white British ancestry UKB —
PSS004469 — —
[
  • 1,171 cases
  • , 6,660 controls
]
 — South Asian — UKB —
PSS004470 — —
[
  • 8,934 cases
  • , 58,491 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)